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Physical and projected pairs of quasars.
No full textQuasars are the most luminous type of active galactic nuclei and their study is fundamental to shed light on the high redshift Universe. In this work we take advantage of the rare cases of close projected and physical quasar pairs to detect the presence of the cool enriched gas and of the dark mass that surround quasars.
This Thesis consists of two parts. In the first one we present optical spectroscopy of projected quasar pairs (i.e., two quasars that are close in the sky but have discordant redshifts) that represents a powerful tool to investigate the metal absorption lines imprinted on the spectrum of the background quasar by the gaseous halo surrounding the foreground one (Chapter 1). In the last decades, this technique has been extensively used to detect the haloes of non–active galaxies, but to date no systematic study has been performed in the case of quasars. We selected a sample of 46 projected pairs, with separations ranging from ∼ 50 kpc to ∼ 200 kpc, aimed to assess the presence of Mg II and CIV absorptions systems associated to foreground quasars. In Chapter 2 we show the first outcomes of our programme, based on the spectra of 13 pairs partially collected by me at the ESO Very Large Telescope (VLT). These data reveal a high covering fraction for the Mg II absorbers and a non isotropical distribution of the gas. Our results are compared to those of similar works performed on non–active galaxies available in the literature. We propose that the cool gaseous haloes of quasars and of normal galaxies are similar, once the stellar mass of the systems is taken into account. Observations of the remaining 33 pairs are ongoing at the Gran Telescopio Canarias (GTC). The preparatory analysis of the SDSS spectra of these systems show that a 10m class telescope is mandatory for this kind of studies (Chapter 3).
The second part of the Thesis addresses with physical systems of quasars (i.e., two or more quasars that have small projected and redshift separations) that are an expected outcome of the current hierarchical framework of galaxy formation and evolution (Chapter 4). In Chapter 5 we accurately study the dynamics of six low redshift quasar pairs and we found that the dynamical mass required for this systems to be gravitationally bound is larger of than the stellar masses of the host galaxies. This suggests that these pairs are hosted by galaxies with massive dark haloes or that they reside in a group/cluster of galaxies. In Chapter 6, we present our discovery of the second physical quasar triplet known to date. We estimate that these systems are extremely rare in terms of simple accidental superposition of the three quasars, suggesting a possible common origin for their ignition. Finally, conclusions and future perspectives of this study are presented in Chapter 7.
The present work principally deals with the analysis and studies presented in Farina et al. (2012b, on the gaseous haloes of quasars), in Farina et al. (2011, on the dynamical study of low redshift quasar pairs), and in Farina et al. (2012c, on the discovery of a new quasar triplet). A complete list of works published during my PhD is provided in Appendix C
Patterns of population structure and adaptive genetic variation in alpine populations of Picea abies (L.) Karst.
Get PDFForest trees dominate many alpine landscapes and are currently exposed to changing climate. Picea abies (L.) Karst (Norway spruce) is one of the most important conifer species of the Italian Alps due to its ecological and economical relevance. Natural populations of this species are found across steep environmental gradients with large differences in temperature and moisture availability. Steep environmental gradients represent interesting models to study the interaction between natural selection and gene flow, especially when aiming to understand adaptation processes under global change. The present work aims to understand adaptive responses to changing climate by determining and quantifying patterns of genetic diversity in natural population of P.abies. a wide array of potential candidate genes was tested, by means of Single Nucleotide Polymorphisms (SNPs), for correlation with climatic and environmental parameters at different spatial scales: i) a geographical scale corresponding to the natural distribution of P.abies across the Italian Alps and ii) at a regional scale on the Eastern Italian Alps. Weak population structure was revealed at the geographical scale with only one population clearly divergent from the unique major genetic cluster identified. At the regional scale, hierarchical analyses of molecular variance revealed that most of the genetic variability was found within populations (ca. 99%), and small but significant variation was also found due landscape features (ca. 0.38%). In order to detect potentially adaptive markers, classical FST outlier approaches were first applied and five outlier loci were revealed at broad scale, while contrasting results were obtained at the regional scale according to the model used. Subsequently, environmental association analysis were performed: at the geographical scale temperature and precipitation were found to influence allelic variation at seven polymorphic loci, while at the regional scale, the Alpine topography resulted a potential adaptive determinants at 19 polymorphic loci, thus considered of ecological relevance. The results obtained in this study may provide relevant information for forestry management and genetic conservation, to understand and quantify the effect of climate change on conifer species as well as their adaptive potential
Solution of the 2D Navier-Stokes equations by a new FE fractional step method.
No full textIn this work, a mathematical and numerical approach for the solution of the 2D Navier-Stokes equations for incompressible fluid flow problems is investigated. A new flux conservative technique for the solution of the elliptic part of the equations is formulated.
In the new model, the non linear convective terms of the momentum equations are approximated by means of characteristics and the spatial approximations, of equal order, are obtained by polynomials of degree two. The advancing in time is afforded by a fractional step method combined with a suitable stabilization technique so that the Inf-Sup condition is respected.
In order to keep down the computational cost, the algebraic systems are solved by an iterative solver (Bi-CGSTAB) preconditioned by means of Schwarz additive scalable preconditioners.
The properties of the new method are verified carrying out several numerical tests. At first, some elliptic, parabolic and convective-diffusive problems are solved and discussed, then the results of some time dependent and stationary 2D Navier-Stokes problems (in particular the well known benchmark problem of the natural convection in a square cavity) are discussed and compared to those found in the literature.
Another, potentially very important application of the numerical tools developed, regards the solution of 1D Shallow-Water equations. In fact the use of the fractional steps scheme for advancing in time and the finite elements (of different polynomial degrees) for the spatial approximation, makes the above mentioned approach computationally profitable and convenient for real applications. The efficiency and accuracy of the numerical model have been checked by solving a theoretical test.
Finally, a brief description of the software suitably developed and used in the tests conclude the thesis
Searching for molecular markers of quality in fish reared in aquaculture.
Get PDFOne of the most unique characteristics of fish as food is that it is highly perishable. Consequently, freshness is fundamental to the quality of fish, and the time that has passed after catching it and the temperature ‘‘history” of fish are very often the key factors in determining the ultimate quality characteristics of such products. Therefore, the development of reliable methods to assess the freshness of fish, as well as the evaluation of quality, has been the goal of fish research for many years.
During post mortem storage, fish muscle degrades and the flesh quality decreases rapidly, depending on the fish species. Loss of freshness, followed by spoilage, is the result of complex biochemical and microbiological processes that begin with a metabolic shift from an aerobic to an anaerobic state. This is followed by transformation of glycogen into lactic acid and the consequent reduction in pH and activation of different proteolytic reactions catalyzed by endogenous enzymes, which produce nutrients that promote subsequent bacterial proliferation. Post mortem tenderization is one of the most unfavourable quality changes in fish muscle and contrasts with mammalian and avian meats in which post mortem degradation of myofibrillar and cytoskeletal proteins is often desired to obtain a tender product.
Previous studies on fish have investigated post mortem phenomena using chemical, physical, histological, and microbiological methods by focusing on indicators such as pH, lactic acid, adenine nucleotides and their degradation products, texture, firmness, and elasticity. Only few studies in the current literature have included a combination of molecular and proteomic investigation. Therefore the objective of the present Thesis was to investigate by molecular biology and proteomic techniques on how different methods of slaughtering and post mortem storage conditions influence the freshness quality of fish filet. The target species was cultured European sea bass (Dicentrarchus labrax) which is a marine teleost of great interest for Mediterranean aquaculture, representing an excellent fishfood product of high commercial value.
Firstly, microfluidic capillary electrophoresis and real-time PCR were successfully applied to investigate the post mortem alterations in RNA extracted from sea bass muscular tissue in relation to three parameters: slaughtering method, and post mortem time and storage temperature (Chapter 3). In the course of this study, we first identified the sea bass cDNA sequences coding for endogenous proteases such as calpains and cathepsins which are assumed to play a major role in post mortem degradation of fish muscle. Then we determined the total RNA and ì-calpain- and cathepsin-L-specific mRNAs integrity over 5 days of storage at two different temperatures (1°C and 18°C) in sea bass slaughtered by three different methods (asphyxia in air, hypothermia/asphyxia in ice, and spinal cord transection). The results of this study showed that, RNA degradation is a slow process under the conditions investigated and, although post mortem storage temperature negatively affects the integrity of total RNA (higher degradation at 18°C), the transcripts of ì-calpain and cathepsin L are present for up to 5 days post mortem in the muscle of sea bass stored at either 1°C or 18°C without showing any significant slaughtering method-related degradation rates.
In the light of these results, and in order to shed light on the influence of temperature on the status of sea bass muscle proteins during post mortem storage, a 2-D DIGE (2 Dimensional Difference Gel Electoforesis) and mass spectrometry study was performed on fish (Chapter 4). As expected, the greatest alterations in sea bass filet protein composition were observed upon post mortem storage at 18°C, with distinct changes appearing in the 2-D protein profile after 5 days of storage at this temperature. In particular, degradation of the myofibrillar protein myosin heavy chain and of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, among the most abundant muscle proteins, could be clearly observed upon storage at higher temperatures. Although to a lesser extent, however, several proteins were observed to vary in abundance also upon storage for 5 days at 1°C. In particular, one of the most interesting observations was the rapid and significant decrease in the abundance of nucleoside diphosphate kinase B and phosphoglycerate mutase 2, which was observed also at low storage temperatures and appeared to be temperature-independent. The results of this study offer new knowledge on changes occurring in sea bass muscle proteins during post mortem storage at different temperatures and provide indications on protein degradation trends that might be useful for monitoring freshness of fish and quality of storage conditions.
Thirdly, 2D DIGE and mass spectrometry were applied to investigate the impact of slaughtering on the post mortem integrity of muscle tissue proteins in European sea bass (Chapter 5). Three different slaughtering techniques were evaluated: asphyxia in air (AA), asphyxia in ice (AI), and spinal cord severance (SCS). Principal components analysis (PCA) revealed a significant divergence of SCS samples, whereas AA and AI samples, although grouped separately, were less divergent and could be included in a single asphyxia cluster. In terms of single proteins, the most significant impact was seen on nucleoside diphosphate kinase B, which was consistently less affected when fish were slaughtered by SCS as compared to asphyxia. Integrity of the sarcomeric proteins myosin heavy chain and myosin binding protein C and of the cytosolic proteins fructose biphosphate aldolase, glyceraldehyde 3-phosphate dehydrogenase, and enolase 1 was also better preserved upon SCS slaughtering. Most interestingly, the influence on muscle protein integrity could be detected since the early post mortem phase. The results of this study demonstrated that slaughtering by SCS preserves protein integrity better than death by asphyxia, either in ice or in air. Both asphyxia conditions are comparably more adverse than SCS to muscle protein integrity, although a general trend favoring AI over AA is observed.
The last objective of this Thesis was to realize a proteome map of the sea bass muscle (Chapter 6) for use in traceability and species authenticity studies, and as a reference for identification of possible freshness and quality markers.
In the last study of this Thesis, the proteome profile of European sea bass (D.labrax) muscle was analyzed using 2-DE and tandem mass spectrometry (MS/MS) with the aim of providing a more detailed characterization of its specific protein expression profile. A highly populated and well resolved 2-DE map of the sea bass muscle tissue was generated, and the corresponding protein identity was provided for a total of 54 abundant protein spots. Upon Ingenuity Pathway Analysis, the proteins mapped in the sea bass muscle profile were mostly related to glycolysis and to the muscle myofibril structure, together with other biological activities crucial to fish muscle metabolism and contraction, and therefore to fish locomotor performance. The data obtained in this study provide important and novel information on the sea bass muscle tissue-specific protein expression, which can be useful for future studies aimed to improve seafood traceability, food safety/risk management and authentication analysis.
In conclusion, the results of this Thesis indicate that, storage conditions are important for post mortem deterioration of fish muscle, and temperature is one of the factors with the strongest impact on this process.
Pre-slaughter and slaughter stressful practices can have an important effect on the fish flesh quality. Therefore, the reduction of stress at slaughter might be a satisfactory strategy for both animal welfare and product quality.
The molecular and proteomic methods used in this Thesis helped to identify nucleoside diphosphate kinase B and phosphoglycerate mutase 2 as candidate biomarkers for the evaluation of sea bass fillet freshness quality
Functional analysis of the human RNASET2 gene: non-cell autonomous tumor suppression and putative stress-induced cell autonomous boles.
Get PDFRNASET2 is an atypical tumor suppressor gene, which behaves as a member of the "tumor antagonizing/malignancy suppressor genes" class. Indeed, in our recent works we have demonstrated that RNASET2 overexpression in ovarian cancer cells is associated with a strong suppression of their tumorigenicity in vivo, without affecting any in vitro cancer-related growth parameter. Noteworthy, the control of tumor growth apparently relies on a non-cell autonomous mechanism which involves the establishment of a cross-talk between RNASET2-overexpressing cancer cells and the tumor microenvironment, where the monocyte/macrophage lineage turned out to represent the most likely target of RNASET2 activity.
Within this framework, the principal aim of my Ph.D. project was to investigate the putative occurrence of a functional cross-talk between the RNASET2-overexpressing tumor cell and the innate immune target cells.
I demonstrate here that RNASET2 protein binds the monocyte/macrophage cell surface via a receptor-mediated interaction and exerts a chemotactic activity on this cell lineage. Thus, I propose that the recruitment and the functional activation of such cells within the tumor microenvironment could be responsible for the RNASET2-mediated tumor suppression that occurs in vivo.
Moreover, I present here data demonstrating both the overexpression and sub-cellular re-localization of RNASET2 protein in response to different stress-inducing treatments. Thus, as for other members of the T2 ribonucleases family, I propose that human RNASET2 could play a cell autonomous role in orchestrating defense mechanisms against stress conditions.
Collectively, these data suggest that at the tumor microenvironment level human RNASET2 could act as an "alarmin", both overexpressed and secreted during the early stages of tumor progression in order to activate innate immune defense mechanisms against the tumor
Integrated experimental and theoretical study of surface properties of TiO2 nanoparticles.
No full textNanostructured titania is rising an increasing interest as one of the key materials for the actual setting of sustainable processes based on the use of sunlight as source of energy. A relevant target is the disclosure of the main structural and surface features that can rule the performances of titania. In this respect, this Ph.D. thesis has been devoted to the study of surface properties of TiO2 nanoparticles with the combined use of IR spectroscopy of adsorbed probe molecules/groups (OH/H2O, CO) and theoretical modeling.
The experimental study of the TiO2 surface sites, with a relevant role for the surface chemistry, allowed to individuate some vibrational bands, due to surface defective sites of TiO2 P25 (Degussa), a kind of benchmark for the photocatalytic applications of titania.
The use of this material represents a source of complexity in this kind of investigations, since the roughness of nanocrystals borders causes the presence of a wide heterogeneity of surface sites with different local structures. Therefore, a TiO2 sample with nanoparticles of regular shape and exposing defined surfaces, has been studied. The a priori knowledge of the surface sites structure has allowed the unambiguous assignment of some of the vibrational bands of the IR spectra of adsorbed probe molecules. These data have been used as reference for the simulation of the IR spectra of adsorbed CO, that allowed the assignment of other signals not attributed on the only basis of experimental data.
The role of the TiO2 surface has also been studied through the TiO2-biomolecules interaction, that provided evidence of the catalytic role of TiO2 surface in promoting the formation of peptidic bond among adsorbed biomolecules
A new isoform of peptide transporter PepT1 (sbPepT1) and ion channels in touch sensation.
No full textPepT1 is an electrogenic transporter expressed at the small intestinal brush-border membrane. It transports di- and tripeptides derived from diet using a H+-electrochemical gradient as driving force. The characterization of the oligopeptide transporters is important not only in nutrition science but also in drug delivery because these proteins are also able to transport a large number of peptido-mimetic drugs and therefore they are responsible for the high levels of oral bioavailability of many pharmaceutical compounds. Examples of PepT1 substrates include angiotensin-converting enzyme (ACE) inhibitors, anticancer drugs, penicillin and cephalosporin antibiotics and the antiviral agents Acyclovir.
The research of my PhD was focused on an sea bass isoform PepT1 cloned at the University of Insubria from the intestine of sea bass (Dicentrarcus labbrax).
The injection of cRNA into Xenopus laevis oocytes allows to obtain a high functional membrane expression of the protein that can be investigated with the use of electrophysiological techniques.
Biophysical and kinetics features of the sea bass oligopeptides transporter 1 were characterized with the two electrode voltage clamp. Exposure of the oocytes to external solutions at different pHs, to substrate concentrations (between 0.03 and 10 mM) and at different membrane voltages allowed to investigate kinetic values as the maximal current (Imax) and the substrate apparent affinity (K0.5).
sbPepT1, as other peptide transporters, exhibits transport-associated currents when different di- and tripeptides are applied to the external solution and presteady-state currents in the absence of substrate.
To better understand the structure-function relation of sbPepT1, the research was extended to the other oligopeptide transporters classes (zebrafish and mammalian). The comparison of the PepT1 transport cycles among the three considered species showed a similar effect of external pH. In fact the presteady-state currents analysis presented a positive shift in the Q/V and τ/V curves and a slowing down of the decay time constants induced by acidity in all the three tested isoforms, especially in the rabbit transporter. These data were used to propose a new kinetic model.
The simulation curves of the presteady-state and the transport currents calculated with the new model that includes the effect of the acidification of external environment were in good agreement with the experimental data
